Dot1-dependent histone H3K79 methylation promotes the formation of meiotic double-strand breaks in the absence of histone H3K4 methylation in budding yeast

Abstract

Epigenetic marks such as histone modifications play roles in various chromosome dynamics in mitosis and meiosis. Methylation of histones H3 at positions K4 and K79 is involved in the initiation of recombination and the recombination checkpoint, respectively, during meiosis in the budding yeast. Set1 promotes H3K4 methylation while Dot1 promotes H3K79 methylation. In this study, we carried out detailed analyses of meiosis in mutants of the SET1 and DOT1 genes as well as methylation-defective mutants of histone H3. We confirmed the role of Set1-dependent H3K4 methylation in the formation of double-strand breaks (DSBs) in meiosis for the initiation of meiotic recombination, and we showed the involvement of Dot1 (H3K79 methylation) in DSB formation in the absence of Set1-dependent H3K4 methylation. In addition, we showed that the histone H3K4 methylation-defective mutants are defective in SC elongation, although they seem to have moderate reduction of DSBs. This suggests that high levels of DSBs mediated by histone H3K4 methylation promote SC elongation.

Figure 1. Dot1 plays a meiotic role in the absence of Set1.

(A) Schematic representation of events during meiosis. (B, C) Spore viability of various strains was measured by dissecting spores. Spores were incubated at 30°C for 3 days. Each bar indicates percentage of spore viability and actual number of total dissected tetrads (parenthesis). Distribution of viable spores per tetrad is shown in (C). Wild type, NKY1303/1543; set1 mutant, MBY015/016; dot1 mutant, MBY005/006; set1 dot1 double mutant, MBY037/039. (D) Meiotic cell division I was analyzed by DAPI staining of wild type (blue circles; NKY1303/1543), dot1 (green circles; MBY005/006), set1 (purple triangles; MBY005/006 and set1 dot1 (red triangle; MBY037/039) mutant cells. At least 150 cells were counted by DAPI staining for each time point. Plotted values are the mean values with standard deviation (S.D.) from four independent time courses. (E) Expression of various meiotic proteins was verified by western blotting. At each time point, cells were fixed with TCA and cell lysates were subject to the analysis. Representative images are shown. Phosphorylated species of Zip1, Hop1, Rec8, and Clb1 are shown by arrows. Wild type, NKY1303/1543; set1, MBY015/016; dot1, MBY005/006; set1 dot1 double mutant, MBY037/039.

Figure 2. Set1 is necessary for meiotic recombination.

(A) Schematic representation of the HIS4-LEU2 locus. Sizes of fragments for DSB and recombinant analysis are shown with lines below. (B) DSB formation and repair at the HIS4-LEU2 locus in different strains were verified by Southern blotting. The experiments were independently performed several times and representative blots are shown. Genomic DNAs were digested with PstI. (C) Formation of crossovers and no-crossovers was also analyzed. The experiments were independently performed several times and representative blots are shown. Genomic DNAs were digested with MluI and XhoI. (D) The bands of DSB I (top left) and DSB II (top right), R1 (crossovers; CO; bottom right), R2 (CO; bottom middle) and R3 (non-crossovers; NCO; bottom left) and were quantified. The symbols represent the wild type (blue circles; NKY1303/1543), dot1 mutant (green circles; MBY005/006), set1 mutant (purple triangles; MBY015/016) and set1 dot1 mutant (red triangle; MBY037/039). Plotted values are the mean values with standard deviation (S.D.) from three independent time courses.

Figure 3. Dot1 promotes Rad51-focus formation in the absence of Set1.

(A) Immunostaining analysis of Rad51 (green) and Dmc1 (red) for wild type (NKY1303/1543), dot1 (MBY005/006), set1 (MBY015/016) and set1 dot1 (MBY037/039) mutant strains was carried out. The bar indicates 2 µm. (B) Kinetics of Rad51 (left) or Dmc1 (right)-focus positive cells in various strains. A focus-positive cell was defined as a cell with more than 5 foci. More than 100 nuclei were counted at each time point. The symbols represent the wild type (blue circles; NKY1303/1543), dot1 mutant (green circles; MBY005/006), set1 mutant (purple triangles; MBY015/016), and set1 dot1 mutant (red triangle; MBY037/039). (C) A number of foci of Rad51 were counted in different strains. The symbols represent the wild type (blue circles; NKY1303/1543), dot1 mutant (green circles; MBY005/006), set1 mutant (purple triangles; MBY015/016), and set1 dot1 mutant (red triangle; MBY037/039). The average number of foci per positive nucleus with S.D. is shown on top. (D) Immunostaining analysis of Rad51 (green) for the dmc1 mutant (MBY009/010), dmc1 dot1 mutant (MBY003/004), dmc1 set1 mutant MBY021/022), and dmc1 set1 dot1 mutant (MBY282/285) was carried out. The bar indicates 2 µm. (E) Meiotic cell division I was analyzed by DAPI staining of the dmc1 mutant (blue circles; MBY009/010), dmc1 dot1 mutant (green circles; MBY003/004), dmc1 set1 mutant (purple triangles; MBY021/022), and dmc1 set1 dot1 mutant (red triangle; MBY282/285) cells. At least 150 cells were counted by DAPI staining for each time point. (F) Kinetics of Rad51-focus positive cells in the dmc1 mutant (blue circles; MBY009/010), dmc1 dot1 mutant (green circles; MBY003/004), dmc1 set1 mutant (purple triangles; MBY021/022), and dmc1 set1 dot1 mutant (red triangle; MBY282/285) strains. A focus-positive cell was defined as a cell with more than 5 foci. More than 100 nuclei were counted at each time point. (G) The number of Rad51 foci was counted in different strains as described above. The average numbers of foci per a Rad51-foci positive nucleus with S.D. is shown on top.

Figure 4. Dot1 promotes the formation of DSBs in the absence of Set1.

(A) Distribution of DSBs along Chromosome III was analyzed by PFGE followed by indirect labeling of one chromosome end using the CHA1. Samples from meiotic time courses of the dmc1 mutant (MSY2630/2632), dmc1 dot1 mutant (MBY003/004), dmc1 set1 mutant (MBY021/022), and dmc1 set1 dot1 mutant (MBY282/285) were analyzed. Band positions used for the quantification in (C) are shown on right. On left, approximate size of chromosomes and the position of two recombination hotspots, HIS4-LEU2 and THR4 are indicated. Green bars on the right side are a possible “Dot1”-dependent DSB bands. (B) Distribution of DSBs along Chromosome VII was analyzed by PFGE followed by indirect labeling of one chromosome end using the CUP2. Band positions used for the quantification in (D) are shown on right. (C) Quantification of DSB frequencies at defined positions on chromosome III were carried out for the dmc1 mutant (Blue bars, MSY2630/2632), dmc1 dot1 mutant (Green Bars, MBY003/004), dmc1 set1 mutant (purple bars, MBY021/022), and dmc1 set1 dot1 mutant (red bars, MBY282/285). Total amounts of DSBs along the chromosome are also shown in right. Plotted values are the mean values with standard deviation (S.D.) at 7 h from three independent time courses. (D) Quantification of DSB frequencies at defined positions on chromosome VII were carried out as shown in (C). Plotted values are the mean values standard deviation (S.D.) at 7 h from two independent time courses. (E) Schematic representation of the YCR047C/CR048W locus. Sizes of fragments for DSB are shown with lines below. (F) DSB formation at the YCR047C/CR048W locus in different strains was verified by Southern blotting. Genomic DNAs were digested with BglII. (G) The bands of DSBs I (left) and II (right) at the YCR047C/CR048W locus were quantified. The experiments were independently performed three times and representative blots are shown. The symbols represent the dmc1 (blue circles; MSY2630/2632), dmc1 dot1 mutant (green circles; MBY003/004), dmc1 set1 mutant (purple triangles; MBY021/022) and dmc1 set1 dot1 mutant (red triangle; MBY282/285). Plotted values are the mean values with standard deviation (S.D.) from three independent time courses.

Figure 5. Set1 promotes the formation of synaptonemal complex.

(A) Immunostaining analysis of chromosome proteins, Zip1 (red) and Hop1 (green), was carried out for wild type and different mutant strains. Representative images are shown for each strain. Representative images for parallel Hop1 lines in the set1 mutants are shown in right. White arrows indicate polycomplexes of Zip1. Wild type, NKY1303/1543; set1 mutant, MBY015/016; dot1 mutant, MBY005/006; set1 dot1 double mutant, MBY037/039. The bar indicates 2 µm. (B) Zip1 staining in wild type and mutant strains was classified as follows: dot (dots I, blue), partial linear (short lines, green), full SC (long lines, red). More than 100 nuclei were counted at each time point. Wild type, NKY1303/1543; set1 mutant, MBY015/016; dot1 mutant, MBY005/006; set1 dot1 double mutant, MBY037/039. (C) Kinetics of spreads with Zip1-PCs were analyzed. Wild type, blue circles; set1 mutant, green circles; dot1 mutant, purple triangles; set1 dot1 double mutant, red triangles. (D) Kinetics of spreads positive for Hop1 were verified in different strains. Wild type, blue circles; set1 mutant, green circles; dot1 mutant, purple triangles; set1 dot1 double mutant, red triangles. (E) Hop1-staining in different strains was classified: short lines (green) and long lines (red). Positive cells for each class were counted. More than 100 nuclei were counted at each time point.

Figure 6. Set1 promotes normal assembly of chromosome axes.

(A) Immunostaining analysis of chromosome proteins, Red1 (red) and Rec8 (green), were carried out for wild type and different mutant strains. Representative images for pachytene (wild type dot1) and pseudo-pachytene (set1 and set1 dot1) stages are shown for each strain; wild type 5 h; the dot1, 5h; the set1, 6 h; the set1 dot1, 6 h. White arrows in the set1 or set1 dot1 mutants shows Rec8/Red1 aggregates. An image for Rec8/Red1 aggregates in the set1 dot1 mutant is enlarged and shown in right. Wild type, NKY1303/1543; set1 mutant, MBY015/016; dot1 mutant, MBY005/006; set1 dot1 double mutant, MBY037/039. The bar indicates 2 µm. (B) Kinetics of spreads positive for Red1 (right) and Rec8 (left) were verified in different strains. The symbols indicate the wild type (blue circles; NKY1303/1543), dot1 mutant (green circles; MBY005/006), set1 mutant (purple triangles; MBY015/016), and set1 dot1 mutant (red triangle; MBY037/039). (C) Kinetics of spreads with Red1/Rec8-PCs were analyzed. Wild type, blue circles; set1 mutant, green circles; dot1 mutant, purple triangles; set1 dot1 double mutant, red triangles.

Figure 7. Histone H3K4 is critical for DSB and SC formation.

(A) Expression of histone H3K4 trimethylation during meiosis. Western blotting analysis for wild type (NKY1303/1543), hht1,2-K4R (MBY211/218) was carried out using anti-histone H3K4-me3. (B) Meiotic cell division I was analyzed by DAPI staining of wild-type (blue circles; NKY1303/1543), hht1,2-K4R (purple triangles; MBY211/218), and hht1,2-K4R dot1 (red triangles; MBY233/237) strains. At least 150 cells were counted by DAPI staining for each time point. (C) Distribution of viable spores per tetrad in wild-type and hht1,2-K4R dot1 (MBY233/237) strains. For each strain, 100 tetrads were dissected. (D) Immunostaining analysis of Rad51 (green) and Dmc1 (red) for wild type (NKY1303/1543), hht1,2-K4R (MBY211/218), and hht1,2-K4R dot1 (MBY233/237) strains was carried out. The bar indicates 2 µm. (E) Kinetics of Rad51 focus-positive cells in various strains. A focus-positive cell was defined as a cell with more than 5 foci. More than 100 nuclei were counted at each time point. The symbols indicate the wild type (blue circles; NKY1303/1543), hht1,2-K4R (purple triangles; MBY211/218), and hht1,2-K4R dot1 (red triangles; MBY233/237) strains. (F) Rad51 focus numbers per nucleus were counted in different strains. The symbols indicate the wild type (blue circles; NKY1303/1543), hht1,2-K4R (purple triangles; MBY211/218), and hht1,2-K4R dot1 (red triangle; MBY233/237) strains. The average number of foci is shown per positive nucleus. (G) Representative images for staining of Zip1(red) and Hop1(green) in wild-type and mutant strains are shown. Hop1 parallel lines the hht1,2-K4R mutant are shown in a pair of arrows on the right. The bar indicates 2 µm. (H) Zip1-staining was classified into 3 classes: dot (dots, blue), partial linear (short lines, green), and full SC (long lines, red). More than 100 nuclei were counted at each time point Kinetics of spreads (Zip1 polycomplexes) were analyzed. Wild type, NKY1303/1543; hht1,2-K4R, MBY211/218; hht1,2-K4R dot1, MBY233/237. (I) Kinetics of Zip1-PC in different strains. The number of spreads containing Zip1-PC was counted in each strain. The symbols indicate the wild type (blue circles; NKY1303/1543), hht1,2-K4R (purple triangles; MBY211/218), and hht1,2-K4R dot1 (red triangle; MBY233/237) strains.

Figure 8. Histone H3K79 is critical for DSB without Set1.

(A) Expression of histone H3K79-methylation during meiosis. Western blotting analysis for the wild-type (NKY1303/1543) and hht1,2-K79R (MBY151/152) strains was carried out using anti-H3K79-methylation. (B) Distribution of viable spores per tetrad in the hht1,2-K79R (MBY151/152) and set1 hht1,2-K79R (MBY219/221) strains. For each strain, 100 tetrads were dissected. (C) Immunostaining analysis of Rad51 (green) and Dmc1 (red) in wild-type cells at 3 h (NKY1303/1543) and set1 hht1,2-K79R (MBY219/221) cells at 6 h. The bar indicates 2 µm. (D) Rad51 focus numbers per nucleus were counted in different strains. Wild type (blue circles; NKY1303/1543), hht1,2-K79R (green circles; MBY219/221), the set1 (purple triangles; MBY015/016) and hht1,2-K79R set1 (red triangle; MBY219/221). Both the set1 and set1 hht1,2-K79R mutants show delayed appearance of Rad51 foci on chromosomes. Thus, focus numbers of Rad51 at 6 h was measured. The number for the set1 is the same as that in Figure 3C. The average number of foci with SD is shown per positive nucleus.